pipelines.chromake.scripts.paths

pipelines.chromake.scripts.paths

The paths module of chromake contains functions to identify the inputs and the files generated by the chromake pipeline.

Functions

Name	Description
get_all_project_peaks	Get the files necessary for the macs3 rules of all projects.
get_all_sequencings_related_paths	Get the path to the files generated by the pipeline for the samples of all sequencings and projects.
get_project_paths_for_macs	Get the files necessary for the macs2/macs3 rules of a project.
get_sequencings_related_paths	Get the path to the files generated by the pipeline for the samples of a specific sequencing.

pipelines.chromake.scripts.paths.get_all_project_peaks(cfg)

Get the files necessary for the macs3 rules of all projects.

Name	Type	Description	Default
cfg	dict	Dict representing the configuration of an analysis with the chromake pipeline.	required

Name	Type	Description
		A list of files outputed by macs2 or macs3

pipelines.chromake.scripts.paths.get_all_sequencings_related_paths(cfg, mode)

Get the path to the files generated by the pipeline for the samples of all sequencings and projects.

Name	Type	Description	Default
cfg	dict	Dict representing the configuration of an analysis with the chromake pipeline.	required
mode	str	String representing the files to get. Accepted values are: - sequencing (raw fastq) - multiqc_raw (multiqc report regrouping the fastqc of the raw fastq files) - cutadapt (fastq after adapter trimming) - fastqc_trimmed (fastqc reports after the adapter trimming) - multiqc_trimmed (multiqc report after adapter trimming) - bam (bam files after alignment with bowtie2) - bam_filtered_coord (bam files after filtering the non-standard chromosomes and sorted by coordinate) - bam_filtered_name (bam files after filtering the non-standard chromosomes and sorted by name) - bedgraph (bedGrapg files generated by HOMER for UCSC visualisation)	required

Name	Type	Description
	list	A list of file paths.

pipelines.chromake.scripts.paths.get_project_paths_for_macs(
    cfg,
    project_name,
    mode,
)

Get the files necessary for the macs2/macs3 rules of a project.

Name	Type	Description	Default
cfg	dict	Dict representing the configuration of an analysis with the chromake pipeline.	required
project_name	str	String representing the name of the project in cfg	required
mode	str	String indicating the output. Accepted values are: - macs (dict with all inputs and the outputs of the macs3 command for all samples associated with the project) - macs_output (list of all outputs of the macs3 command for the project)	required

Name	Type	Description
		A dictionary of all file paths for the project.

pipelines.chromake.scripts.paths.get_sequencings_related_paths(
    cfg,
    sequencing_name,
    mode,
)

Get the path to the files generated by the pipeline for the samples of a specific sequencing.

Name	Type	Description	Default
cfg	dict	Dict representing the configuration of an analysis with the chromake pipeline.	required
sequencing_name	str	String representing the name of the sequencing	required
mode	str	String representing the files to get. Accepted values are: - sequencing (raw fastq) - multiqc_raw (multiqc report regrouping the fastqc of the raw fastq files) - cutadapt (fastq after adapter trimming) - fastqc_trimmed (fastqc reports after the adapter trimming) - multiqc_trimmed (multiqc report after adapter trimming) - bam (bam files after alignment with bowtie2) - bam_filtered (bam files after filtering the non-standard chromosomes) - flagstat (output of samtools flagstat on the bam files) - stats (output of samtools stats on the bam files) - multiqc_stats (multiqc on the folder containing the stats output)	required

Name	Type	Description
	list	A list of all file paths.